李海鹏 - 中国科学院上海营养与健康研究所 -

个人简介

2007-至今中国科学院-马普学会计算生物学伙伴研究所研究员 2003-2007年德国慕尼黑大学、科隆大学博士后 2002-2003年美国德克萨斯大学博士后 1996-2002年中国科学院昆明动物所博士 1992-1996年山东大学学士

研究领域

研究适应性进化理论及分子机制开发检测算法，长期致力于群体遗传学和生物信息学方面的研究工作。在群体遗传学方面，我们的目标是研究生物（比如人、果蝇和病原体等）中由于近期正选择(达尔文适应性进化)而产生的适应现象，避免因群体进化历史、遗传重组的干扰而导致检测结果的高假阳性。这些研究能够帮助我们了解基因的功能以及基因和环境的相互作用。我们希望了解自然选择是如何帮助人类适应环境的变化，特别是自然选择如何加速了意识和语言的产生。在生物信息学领域，我们研发普适性的软件分析平台以面对基因数据分析的各种需求。

近期论文

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1. Lin Zeng, Chen Ming, Yan Li, Ling-Yan Su, Yan-Hua Su, Newton O. Otecko, Ambroise Dalecky, Stephen Donnellan, Ken Aplin, Xiao-Hui Liu, Ying Song, Zhi-bin Zhang, Ali Esmailizadeh, Saeed S. Sohrabi, Hojjat Asadollahpour Nanaei, He-Qun Liu, Ming-Shan Wang, Solimane Ag Atteynine, Gerard Rocamora, Fabrice Brescia, Serge Morand, David M. Irwin, Ming-sheng Peng, Yong-Gang Yao, Haipeng Li*, Dong-Dong Wu*, Ya-Ping Zhang* (2018) Out of southern East Asia of the brown rat revealed by large scale genome sequencing. Mol. Biol. Evol. 35:149-158 (cover story). 2. Zongfeng Yang, Junrui Li, Thomas Wiehe, Haipeng Li* (2018) Detecting recent positive selection with a single locus test bi-partitioning the coalescent tree. Genetics DOI:10.1534/genetics.117.300401 3. Jiang-An Yin, Ge Gao, Xi-Juan Liu, Zi-Qian Hao, Kai Li, Xin-Lei Kang, Hong Li, Yuan-Hong Shan, Wen-Li Hu, Haipeng Li, Shi-Qing Cai* (2017) Genetic variation in glia-neuron signalling modulates ageing rate. Nature 551(7679): 198-203. 4. Lin Zeng, Chen Ming, Yan Li, Ling-Yan Su, Yan-Hua Su, Newton O. Otecko, He-Qun Liu, Ming-Shan Wang, Yong-Gang Yao, Haipeng Li, Dong-Dong Wu, and Ya-Ping Zhang (2017) Rapid evolution of genes involved in learning and energy metabolism for domestication of the laboratory rat. Mol. Biol. Evol. 34(12): 3148-3153. 5. Lei Chen, Jing Yang, Zhihao Xing, Fei Yang, Yang Shu, Yunhua Zhang, Xiangyin Kong, Tao Huang, Haipeng Li*, Yudong Cai* (2017) An integrated method for the identification of novel genes related to oral cancer. PLoS ONE 12:e0175185. 6. Haipeng Li？, Jinggong Xiang-Yu？, Guangyi Dai, Zhili Gu, Chen Ming, Zongfeng Yang, Oliver A. Ryder, Wen-Hsiung Li, Yun-Xin Fu, Ya-Ping Zhang (2016) A large number of vertebrates began rapid population decline in the late 19th century. Proc Natl Acad Sci USA 113:14079-14084. 7. Jinggong Xiang-Yu, Zongfeng Yang, Kun Tang, Haipeng Li* (2016) Revisiting the false positive rate in detecting recent positive selection. Quantitative Biology 4:207–216. 8. Feng Gao, Chen Ming, Wangjie Hu, Haipeng Li* (2016). New software for the fast estimation of population recombination rates (FastEPRR) in the genomic era. G3-Genes Genomes Genetics 6:1563-1571. 9. Tiao Ning, Jing Li, Kao Lin, Heng Xiao, John S. Wylie, Hua Shun, Haipeng Li*, Yaping Zhang* (2014). Complex evolutionary patterns revealed by mitochondrial genomes of the domestic horse. Current Molecular Medicine 14(10):1-13. 10. Kao Lin, Andreas Futschik, Haipeng Li* (2013) A fast estimate for the population recombination rate based on regression. Genetics 194:473-484. 11. Haipeng Li, Thomas Wiehe (2013) Coalescent tree imbalance and a simple test for selective sweeps based on microsatellite variation. PLoS Computational Biology 9: e1003060. 12. Bi-Qing Li, Jin You, Lei Chen, Jian Zhang, Ning Zhang, Haipeng Li, Tao Huang, Xiang-Yin Kong and Yudong Cai (2013) Identification of lung cancer related genes with the shortest path approach in a protein-protein interaction network. BioMed Research International 2013:267375 13. Bing Niu, Xiaocheng Yuan, Preston Roeper, Qiang Su, Chunrong Peng, Jingyuan Yin, Juan Ding, Haipeng Li*, Wencong Lu (2013). HIV-1 protease cleavage site prediction based on two-stage feature selection method. Protein & Peptide Letters 20:290-298. 14. Shen Niu, Tao Huang, Kaiyan Feng, Zhisong He, Weiren Cui, Lei Gu, Haipeng Li, Yudong Cai, Yixue Li (2013). Inter- and intra-chain disulfide bond prediction based on optimal feature selection. Protein & Peptide Letters 20:324-335. 15. Li, H.* (2012) Beyond our naked eyes. Journal of Molecular Cell Biology 4:63. 16. Li, Z. H., Zou, J., Mao, K., Lin, K., Li, H., Liu, J., Kallman, T., Lascoux, M. (2012) Population genetic evidence for complex evolutionary histories of four high altitude Juniper species in the QinHai-Tibetan Plateau. Evolution 66:831-845. 17. Wang, K., Hu, L., Shi, X., Dong Y., Li, H.*, Wen, T. (2012) PSCL: Predicting protein subcellular localization based on optimal functional domains. Protein & Peptide Letters 19:15-22. 18. Li, J., Li, H., Jakobsson, M., Li, S., Sjodin, P., Lascoux, M. (2012). Joint analysis of demography and selection in population genetics: where do we stand and where could we go? Molecular Ecology 21:28-44. 19. Huang, T., Wan, S., Xu, Z., Zheng, Y., Feng, K. Y., Li, H.*, Kong, X., Cai, Y. (2011). Analysis and prediction of translation rate based on sequence and functional features of the mRNA. PLoS ONE 6:e16036. 20. Hu, L., Li, Z., Wang, K., Niu, S., Shi, X. H., Cai, Y. D. and Li, H.* (2011) Prediction and analysis of protein methylarginine and methyllysine based on multisequence features. Biopolymers 95:763-771. 21. Lin, K., Li, H.*, Schlotterer, C., Futschik, A. (2011). Distinguishing positive selection from neutral evolution: boosting the performance of summary statistics. Genetics 187:229-244. 22. Li, H.* (2011). A new test for detecting recent positive selection that is free from the confounding impacts of demography. Mol Biol Evol 28:365-375. 23. Chen, L., Feng. K., Cai, Y., Chou, K., Li, H.* (2010). Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. BMC Bioinformatics 11:293. 24. Lin, K., Qiang, Z., Lu, L., Lu, L.-Y., Lai, L., Gu, J., Zeng, Z., Li, H.*, and Cai., Y. (2010). Predicting miRNA's target from primary structure by the nearest neighbor algorithm. Mol Divers 14:719-729. 25. Li, J., Yang, H., Li, J.-R., Li, H., Ning, T., Pan, X.-R., Shi, P., and Zhang, Y.-P. (2010) Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication. Heredity 105:274-281. 26. Lu, L., Lin, K., Qian, Z., Li, H.*, Cai, Y.-D., Li, Y. (2010). Predicting DNA methylation status using word composition. J. Biomedical Science and Engineering 3:672-676. 27. Lu, L, Shi, X, Li, S.-J., Xie, Z.-Q., Feng, Y.-L., Lu, W.-C., Li. Y., Li, H.* and Cai, Y.-D. (2010) Protein sumoylation sites prediction based on two-stage feature selection. Molecular Diversity, 14:81-86. 28. Lu, L. Y., Qian, Z., Shi, X., Li, H., Cai, Y.-D., and Li, Y. (2010) A knowledge-based method to predict the cooperative relationship between transcription factors. Molecular Diversity, 14:815-819. 29. Lin, K. and Li, H*. (2009) Advances in detecting positive selection on genome. Hereditas, 31: 896-902. 30. Xu, H., Li, J. and Li, H.* (2009) Application of differential equation to the evolution of two groups. Zoological Research, 30, 11-16. 31. Zhang, W., Cai, W.-W., Zhou, W.-P., Li, H., Li, L., Yan, W., Deng, Q.-K., Zhang, Y.-P., Fu, Y.-X. and Xu, X.-M. 2008. Evidence of gene conversion in the evolutionary process of the codon 41/42 (-CTTT) mutation causing β-Thalassemia in Southern China. J Mol Evol 66:436-445. 32. Stephan, W. and Li, H. 2007. The recent demographic and adaptive history of Drosophila melanogaster. Heredity 98:65-68. 33. Hutter, S., Li, H., Beisswanger, S., De Lorenzo, D. and Stephan, W. 2007. A scan of autosomal sequence variation in D. melanogaster. Genetics 177:469-480. 34. Li, H. and Stephan, W. 2006. Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet 2:e166. 35. Li, H. and Stephan, W. 2005. Maximum-likelihood methods for detecting recent positive selection and localizing the selected site in the genome. Genetics 171:377-384. 36. Zhao, Z., Li, H., Wu, X., Zhong, Y., Zhang, K., Zhang, Y.-P., Boerwinkle, E. and Fu, Y.-X. 2004. Moderate mutation rate in the SARS coronavirus genome and its implications. BMC Evolutionary Biology 4:21. 37. Li, H., Zhang, Y., Zhang, Y.-P. and Fu, Y.-X. 2003. Neutrality tests using DNA polymorphism from multiple samples. Genetics 163:1147-1151. 38. Li, H., Meng, S.-J., Men, Z.-M., Fu, Y.-X. and Zhang, Y.-P. 2003. Genetic diversity and population history of golden monkeys (Rhinopithecus roxellana). Genetics 164:269-275. 39. Zhang, Y.-P., Wang, X.-X., Ryder, O. A., Li, H., Zhang, H.-M., Yong, Y. and Wang, P.-Y. 2002. Genetic diversity and conservation of endangered animal species. Pure Appl Chem 74:575-584. 40. Ding, Y. C., Wooding, S., Harpending, H. C., Chi, H. C., Li, H., Fu, Y.-X., Pang, J. F., Yao, Y. G., Yu, J. G., Moyzis, R. and Zhang, Y.-P. 2000. Population structure and history in East Asia. Proc Natl Acad Sci USA 97:14003-14006. 41. Wu, C.-H., Li, H., Wang, Y.-X.,and Zhang, Y.-P. 2000. Low genetic variation of the Yunnan hare (Lepus comus G. Allen 1927) as revealed by mitochondrial cytochrome b gene sequences. Biochem Genet 38:149-155. 42. Li, H. and Zhang, Y.-P. 1999. A computer program for analyzing RFLP data from population study. Zoological Research 20:326. 43. Li, H., Zhang, Y.-P., Meng, S.-J., Men, Z.-M., Han, J.-L., Feng, N. and Zhang, G.-Q. 1998. Low genetic diversity in Sichuan snub-nosed monkey revealed by protein electrophoresis and its significance to conservation biology. Zoological Research 19:417-421.